The aviation industry stands as a well-known “hard to electrify” sector, currently responsible for the consumption of massive amounts of fossil fuels, considerably contributing to global CO2 emissions. The need to reduce the aviation carbon footprint to comply with the European Green Deal objectives, has driven intensive research into the so-called bio-jet fuels (BJF) that can be obtained from different lipid-rich substrates, including microalgae among the most promising. Starting from the analysis of existing studies dealing with the selection of the strains more indicated for BJF production, this review examines the most recent breakthrough in microalgae cultivation techniques and lipid accumulation strategies, focusing on the approaches targeting the enhancement of the process environmental sustainability. The main bottlenecks in each phase of the production process are identified and critically reviewed. The most recent solutions are also thoroughly discussed to point out room for improvements in consolidated engineering strategies, as well as areas of further scientific research to advance the state of the art on micro-algal potential for BJF production.